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- PDB-9qfu: Human Tryptase beta-2 (hTPSB2) complexed with covalent inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 9qfu
TitleHuman Tryptase beta-2 (hTPSB2) complexed with covalent inhibitor Compound #1
ComponentsTryptase beta-2
KeywordsHYDROLASE / BETA-TRYPTASE
Function / homology
Function and homology information


tryptase / serine-type peptidase activity / : / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / ACETATE ION / DI(HYDROXYETHYL)ETHER / Tryptase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 Å
AuthorsPorta, A. / Manelfi, C. / Talarico, C. / Beccari, A.R. / Brindisi, M. / Summa, V. / Iaconis, D. / Gobbi, M. / Beeg, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2025
Title: Integrating Surface Plasmon Resonance and Docking Analysis for Mechanistic Insights of Tryptase Inhibitors.
Authors: Porta, A. / Manelfi, C. / Talarico, C. / Beccari, A.R. / Brindisi, M. / Summa, V. / Iaconis, D. / Gobbi, M. / Beeg, M.
History
DepositionMar 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptase beta-2
B: Tryptase beta-2
C: Tryptase beta-2
D: Tryptase beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,41645
Polymers109,0614
Non-polymers5,35541
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.552, 78.552, 165.688
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tryptase beta-2 / Tryptase-2 / Tryptase II


Mass: 27265.131 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Lung / References: UniProt: P20231, tryptase

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Non-polymers , 7 types, 565 molecules

#2: Chemical
ChemComp-A1I52 / ~{N}-[(1~{S},2~{S})-6-azanyl-1-[5-[[4-[2-(3,4-dichlorophenyl)ethoxy]phenyl]methyl]-1,2,4-oxadiazol-3-yl]-1-oxidanyl-hexan-2-yl]-4-fluoranyl-benzamide


Mass: 601.496 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H31Cl2FN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: The protein was formulated as a 2 mg/mL solution in 10 mM MES (pH 6.1) and 2M NaCl, and was crystallized from a solution of 0.1 M NaoAc (pH 4.6), 0.2 M ammonium sulfate and 30% PEG 1500

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.983→62.93 Å / Num. obs: 74832 / % possible obs: 99.64 % / Redundancy: 6.6 % / CC1/2: 0.995 / Net I/σ(I): 7.8
Reflection shellResolution: 1.983→2.017 Å / Num. unique obs: 74832 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
REFMACv.5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
REFMACv.5.8.0267phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.983→62.93 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22074 -5.4 %RANDOM
Rwork0.17677 ---
obs0.17907 74832 99.64 %-
Refinement stepCycle: LAST / Resolution: 1.983→62.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 336 524 8540

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